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- PDB-6dun: Crystal Structure Analysis of PIN1 -

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Basic information

Entry
Database: PDB / ID: 6dun
TitleCrystal Structure Analysis of PIN1
ComponentsPeptidyl-prolyl cis-trans isomerase NIMA-interacting 1
KeywordsISOMERASE / prolyl isomerase
Function / homology
Function and homology information


cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / postsynaptic cytosol / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / negative regulation of amyloid-beta formation ...cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / postsynaptic cytosol / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / negative regulation of amyloid-beta formation / negative regulation of SMAD protein signal transduction / PI5P Regulates TP53 Acetylation / cytoskeletal motor activity / RHO GTPases Activate NADPH Oxidases / phosphoserine residue binding / protein peptidyl-prolyl isomerization / positive regulation of protein dephosphorylation / ciliary basal body / negative regulation of protein binding / regulation of cytokinesis / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Negative regulators of DDX58/IFIH1 signaling / synapse organization / phosphoprotein binding / regulation of protein phosphorylation / negative regulation of transforming growth factor beta receptor signaling pathway / tau protein binding / regulation of protein stability / negative regulation of protein catabolic process / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / neuron differentiation / beta-catenin binding / positive regulation of GTPase activity / positive regulation of canonical Wnt signaling pathway / positive regulation of protein binding / midbody / regulation of gene expression / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / protein stabilization / nuclear speck / cell cycle / positive regulation of protein phosphorylation / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Chitinase A; domain 3 - #40 / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. ...Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Chitinase A; domain 3 - #40 / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Chitinase A; domain 3 / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
TRIHYDROXYARSENITE(III) / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
CitationJournal: Nat Commun / Year: 2018
Title: Arsenic targets Pin1 and cooperates with retinoic acid to inhibit cancer-driving pathways and tumor-initiating cells.
Authors: Kozono, S. / Lin, Y.M. / Seo, H.S. / Pinch, B. / Lian, X. / Qiu, C. / Herbert, M.K. / Chen, C.H. / Tan, L. / Gao, Z.J. / Massefski, W. / Doctor, Z.M. / Jackson, B.P. / Chen, Y. / Dhe- ...Authors: Kozono, S. / Lin, Y.M. / Seo, H.S. / Pinch, B. / Lian, X. / Qiu, C. / Herbert, M.K. / Chen, C.H. / Tan, L. / Gao, Z.J. / Massefski, W. / Doctor, Z.M. / Jackson, B.P. / Chen, Y. / Dhe-Paganon, S. / Lu, K.P. / Zhou, X.Z.
History
DepositionJun 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
B: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4624
Polymers27,2102
Non-polymers2522
Water2,774154
1
A: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7312
Polymers13,6051
Non-polymers1261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7312
Polymers13,6051
Non-polymers1261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.270, 36.210, 51.590
Angle α, β, γ (deg.)90.000, 100.750, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-4154-

HOH

21A-4167-

HOH

31B-4177-

HOH

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 / Peptidyl-prolyl cis-trans isomerase Pin1 / PPIase Pin1 / Rotamase Pin1


Mass: 13605.146 Da / Num. of mol.: 2 / Fragment: PIN1 / Mutation: K77Q, K82Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIN1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13526, peptidylprolyl isomerase
#2: Chemical ChemComp-TAS / TRIHYDROXYARSENITE(III) / Arsenous acid


Mass: 125.944 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AsH3O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 2 M ammonium citrate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2015
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.59→50.685 Å / Num. obs: 28643 / % possible obs: 98.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 8.93
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.59-1.632.71.025198.7
7.11-50.682.80.034197.5

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Processing

Software
NameVersionClassification
XDSdata reduction
xia2data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PIN

1pin


Resolution: 1.59→50.685 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.37
RfactorNum. reflection% reflection
Rfree0.1987 1457 5.09 %
Rwork0.1521 --
obs0.1545 28639 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.75 Å2 / Biso mean: 24.7461 Å2 / Biso min: 9.76 Å2
Refinement stepCycle: final / Resolution: 1.59→50.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 0 14 154 1935
Biso mean--79.13 35.61 -
Num. residues----229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061803
X-RAY DIFFRACTIONf_angle_d0.7682421
X-RAY DIFFRACTIONf_chiral_restr0.048257
X-RAY DIFFRACTIONf_plane_restr0.004325
X-RAY DIFFRACTIONf_dihedral_angle_d15.4061097
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.59-1.64690.35581540.27832691284599
1.6469-1.71280.29911410.22332701284299
1.7128-1.79080.24281460.18812690283699
1.7908-1.88520.2051630.14992692285599
1.8852-2.00330.21431350.12992716285199
2.0033-2.1580.18221330.11772725285899
2.158-2.37510.1731370.11272726286399
2.3751-2.71880.18091490.12692731288099
2.7188-3.42530.18531550.14522718287399
3.4253-50.71040.18621440.1692792293698

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